5DH6 Rna date Aug 29, 2015
title Two Divalent Metal Ions And Conformational Changes Play Role Hammerhead Ribozyme Cleavage Reaction-G12a Mutant In Mg2+
authors A.Mir, J.Chen, D.Neau, B.L.Golden
compound source
Molecule: Hammerhead Ribozyme
Chain: A
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: This Rna Was Made By In Vitro Transcription

Molecule: 5'-R(Gpgpgpcpgpu)-D(Pc)- R(Pupgpgpgpcpapgpupapcpcpcpa)-3';
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthesized Oligonucleotide
symmetry Space Group: C 2 2 21
R_factor 0.211 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.405 85.964 102.969 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.78 Å
ligand MG enzyme
Primary referenceTwo Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction., Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL, Biochemistry. 2015 Oct 2. PMID:26398724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (5dh6.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 5DH6
  • CSU: Contacts of Structural Units for 5DH6
  • Structure Factors (141 Kb)
  • Retrieve 5DH6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DH6 from S2C, [Save to disk]
  • Re-refined 5dh6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DH6 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5DH6
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dh6_B] [5dh6_A] [5dh6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5DH6
  • Community annotation for 5DH6 at PDBWiki (http://pdbwiki.org)

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